Ryan Hernandez

The BMI PhD program @ucsanfrancisco.bsky.social is recruiting! Want to use computing to advance our understanding of biology and disease? Virtual Info Session: Tue 10/27, 1-2pm PT. Learn about our research, our approach to training, and what makes a strong app! Register: tiny.ucsf.edu/BMI2026

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We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

#PEQG26 such a wonderful meeting at Asilomar. Fantastic science, beautiful views, adorable wildlife, great friends! 🫶

1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...

We built a joint experimental and computational platform for scalable multi-modal single-cell chemical screens — profiling RNA, protein (including phospho-signaling), and chromatin accessibility responses to thousands of small molecule perturbations in parallel. www.biorxiv.org/content/10.6...

Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtland’s Warbler www.biorxiv.org/content/10.6...

Accounting for recurrent mutation in the frequency spectrum of rare alleles https://www.biorxiv.org/content/10.64898/2026.05.29.728884v1

This was fitting news to receive on May 1, international workers day. I will be returning to work on Monday after being kept on retaliatory administrative leave for 5 months and 3 weeks. I return along with the brave Katrina Declaration signers from FEMA, also reinstated this week. 🧵1/?

I'm struck by the bravery of this student and the fantastic way the union handled this allegation. What a model for all of us to follow in terms of how to show up for our members.

May have unlocked a new academic cheat code! 14yo kid just read a 2pg application I wrote for an award. They schooled me on proper comma, colon, and semi-colon use. Also helped me clarify a few sentences (no, structural barriers aren't "physically preventing" scholars from participating in science)

🗓️📍Save the date for UCSF PROPEL’s 6th Annual Symposium on June 1st!! 🧑‍🔬🧫Come support and celebrate our scholars as they present research talks and posters! We look forward to seeing you there!

My goodness SF is beautiful. I had never seen a night rainbow before!!! #doLookUp

Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...

David Botstein has passed away. A true pioneer in the genetics and biotechnology industry, known methods to map genes. While at Stanford he collaborated with Pat Brown in microarrays, co-founded the Gene Ontology and became the CSO of Calico. He worked again with Pat Brown at Impossible Foods. RIP.

1. Kevin Gross and I have a new paper out today PLOS Biology. We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

"In particular, these models highlight a pernicious feedback loop: increasing submissions to top journals exhausts the pool of suitable peer reviewers, resulting in lower quality peer reviews that encourage yet more authors to take a chance on submitting their paper to a prestigious venue."

www.biorxiv.org/content/10.6... Glad to see this paper out. I attended Prof. Gürsoy's talk during last year's probgen and the claims were scary. You can literally reverse-engineer GWAS summary statistics and public single-cell RNA-seq data to identify subjects.

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza. Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

🚨 Proud to share that our paper on the genetic links between type 2 diabetes (T2D) and hypertension is now published in @natcomms.nature.com! We dissect the genetic relationship between T2D and hypertension and show it is not driven by a single shared pathway. 🧬 (1/N)

academic.oup.com/genetics/adv... #histbio #hps

My colleagues at @sfsu.bsky.social used 3 decades of data to show that students with low undergrad GPA have equal PhD completion rates compared to students with high GPA. @sfstatebio.bsky.social journals.plos.org/plosone/arti...

Sad. We are a country in decline www.chronicle.com/article/has-... #gradschool #phd

So excited to have this study live! Lead by @ee-reh-neh.bsky.social's teram and in collaboration with an incredible team at MRIN in Indonesia. This is the culmination of ~5 years of work including a ton of effort in the field. Really proud of how this came together! www.biorxiv.org/content/10.6...

Very nice work led @drghawkes.bsky.social, showing convergence between rare and common genetic associations, using whole-genome sequencing data to evaluate the contribution of rare non-coding variants for commonly studied anthropometric traits 🧪🧬 www.nature.com/articles/s41...

Science Bluesky is now much better than Science Twitter is… but I still miss peak pre-pandemic Science Twitter.

My daughter Maya, who had to wear a scoliosis brace for 2 years, wants to connect with other teens who live with invisible diseases. www.under-the-iceberg.com/about

We are in the middle of MCB graduate admissions interviews. It has renewed my sense of hope—there are so many bright, empathic and resilient young people ready to help advance knowledge and make a difference.

It took scientists 11 years to compute 1-2/3=1/3

A new preprint from the lab, with postdoc @deboraycb.bsky.social and collaborators @aidaandres.bsky.social and Tim Connallon: “Characterising the detectable and invisible fractions of genomic loci under balancing selection” www.biorxiv.org/content/10.6...

Hey MD/PhD-bound Scholars 👋 Prepare for MSTP Program applications with PROPEL! This is an opportunity you don't want to miss! 📆 Feb 6 – Sign up for AMCAS essay reviews by MSTP grad students (QR code) 📆 Feb 13 – Submit essay draft for review 📆 Feb 20 – Receive Feedback

PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5! *Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.

The meeting will take place at the gorgeous IslandWood Resort on Bainbridge Island, a short ferry ride from downtown Seattle. Registration is free. We will cover travel and lodging for graduate students, and at least partially subsidize those costs for postdocs and assistant professors.

Excited to share our new preprint from the @arbelharpak.bsky.social Lab! How do recruitment into genetic studies and study characteristics impact what we infer about the genetic bases of traits, and what are the consequences? (1/21) www.biorxiv.org/content/10.6...

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

Here's my latest contribution to the @nytimes "Lost Science" series. Brenna Henn's sweeping study of African genetics has been frozen. Gift link: nyti.ms/3Ypmm1A

Oh come on… it is January SECOND. Who ALREADY broke our cluster?? #Wyntoff

This story is heartbreaking. Brenna Henn is a wonderful scientist, and the work their lab does is truly insightful. Anger and rage… www.nytimes.com/2026/01/02/s...

I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post: substack.com/home/post/p-...

Putting on my hat as @asn-amnat.bsky.social ASN President for a minute for a string of announcements, please share widely!!! 1. Student research awards are open for applications, to fund research expenses for 10 graduate students ($2000 each) nam10.safelinks.protection.outlook.com?url=https%3A...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

What a beautiful paper! www.nature.com/articles/s41...

Our latest preprint revisits the classic model of mutation-selection balance. Do human recessive genes fit Haldane's 100-year old model? This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io www.biorxiv.org/content/10.6...

Normalization of glucose in people with prediabetes, i.e. achieving remission, is linked to halving of major cardiovascular adverse events over ensuing decades www.thelancet.com/journals/lan...